Challenges for Obama's new national security team are huge

He says military may pull back and civilian forces may grow in places such as Afghanistan

Cronin: Managing the tense relationship with Pakistan will be major challenge

Editor's note: Patrick M. Cronin is senior adviser and senior director of the Asia-Pacific Security Program at the Center for a New American Security, a nonpartisan research organization in Washington.

Washington (CNN) -- President Barack Obama's national security shake-up will pit some of America's most able practitioners against some of the nation's most intractable challenges.

The forceful, organized administration troubleshooter Leon Panetta will try to fill the big shoes left by outgoing Defense Secretary Robert M. Gates, who some consider to have been one of America's finest Pentagon chiefs. Balancing military operations with emerging competitors such as China during a period of fiscal austerity will tax Panetta's extensive bureaucratic and budgetary skills.

Gen. David H. Petraeus, who has spent most of the past decade leading the fight in Iraq and Afghanistan, would replace Panetta as director of the CIA, a shift that could presage a growing agency role in the current wars.

Marine Lt. Gen. John Allen will deploy to Afghanistan to replace Petraeus as commander of the International Security Assistance Force and U.S. Forces Afghanistan. His teamwork and strategic acumen (he is a truly distinguished graduate of the National War College) will put him in charge of operations at the beginning of the three-year period ahead in which the administration plans to draw down U.S. forces to make way for far greater reliance on Afghans to lead the security effort.

Meanwhile, Ryan Crocker, who retired from the Foreign Service in 2009, would leave his comfortable position as dean of the Bush School of Government and Public Service at Texas A&M (where Gates was president before being plucked to become defense secretary five years ago). Crocker, the quintessential diplomat-warrior, would become ambassador to Afghanistan, replacing Karl Eikenberry at a time when U.S. relations with President Hamid Karzai have perhaps reached an all-time low.

At stake is whether Pakistan is willing and able to close down terrorist sanctuaries on the Afghan border.--Patrick Cronin

How will these and other key personnel changes (including a new Chairman of the Joint Chiefs of Staff by October) affect the current conflicts and security arena?

First, the new national security team may oversee a military drawdown but a civilian buildup in Afghanistan, Iraq, Libya and perhaps elsewhere. U.S. force levels in Afghanistan are likely to remain fairly high for the near-term, but political and budget pressures will make it difficult for the administration to stray from its plan to begin troop reductions this year in advance of a combat handoff at the end of 2014.

In Iraq, where problems remain despite the completion of front-line combat missions for the United States, civilian contractors who can conduct security and advisory missions will be at a premium. And the desire to avoid boots on the ground in yet a third war, such as Libya, will make it tempting for the Obama administration to revert to what the United States did in the 1950s: namely, rely more heavily on CIA forces to help survey and shape a country in conflict. Certainly the new director of the CIA will be one of the most knowledgeable military minds in the Cabinet.

A second way in which the high-level personnel shift will affect national security will come down to who manages key partnerships. Petraeus will be placed in the position to help salvage one of the hardest yet most consequential relationships that the United States has -- with Pakistan.

Panetta has already earned his stripes in trying to deal with Pakistan's really powerful men -- Army Chief Gen. Ashfaq Parvez Kayani and intelligence chief Lt. Gen. Ahmad Shuja Pasha, head of the Inter-Services Intelligence or ISI.

At stake is whether Pakistan is willing and able to close down terrorist and insurgent sanctuaries on the Afghan border. Tense discussions already have been held this month as Pakistan's security leaders pressured the United States to curtail its use of drones. But it is also disturbing that Pakistan's civilian leaders, including Prime Minister Yusuf Raza Gilani, reportedly encouraged Afghanistan's Karzai to favor ties with Pakistan and China over those to the United States.

Managing the Pakistan relationship well is a vital national interest, and both Panetta and Petraeus will be in the right position to try to do so.

The third impact of the personnel shift will center on budget battles and the tough choices that will have to be made regarding future defense capabilities. Panetta will have to take the lead in defending the military's budget at a time when many in Congress and the public are being asked to accept protracted belt-tightening.

Gates has rightly warned against simple cross-the-board reductions, as budgeting would trump strategy and leave a less able force. For Panetta the crucial question will be how much he can transform the Pentagon business model to make it more efficient to invest in a force that will keep up with rapidly emerging powers such as China.

The opinions expressed in this commentary are solely those of Patrick M. Cronin.